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Physicist, Startup Founder, Blogger, Dad

Tuesday, April 26, 2011

Newsweek on BGI

Newsweek: The world’s largest genome-mapping facility is in an unlikely corner of China. Hidden away in a gritty neighborhood in Shenzhen’s Yantian district, surrounded by truck-repair shops and scrap yards prowled by chickens, Beijing’s most ambitious biomedical project is housed in a former shoe factory.

But the modest gray exterior belies the state-of-the-art research inside. In immaculate, glass-walled and neon-lit rooms resembling intensive care units, rows of identical machines emit a busy hum. The Illumina HiSeq 2000 is a top-of-the-line genome-sequencing machine that carries a price tag of $500,000. There are 128 of them here, flanked by rows of similar high-tech equipment, making it possible for the Beijing Genomics Institute (BGI) to churn out more high quality DNA-sequence data than all U.S. academic facilities put together.

“Genes build the future,” announces a poster on the wall, and there is no doubt that China has set its eye on that future. This year, Forbes magazine estimated that the genomics market will reach $100 billion over the next decade, with scientists analyzing vast quantities of data to offer new ways to fight disease, feed the world, and harness microbes for industrial purposes. “The situation in genomics resembles the early days of the Internet,” says Harvard geneticist George Church, who advises BGI and a number of American genomics companies. “No one knows what will turn out to be the killer apps.” Companies such as Microsoft, Google, IBM, and Intel have already invested in genomics, seeing the field as an extension of their own businesses—data handling and management. “The big realization is that biology has become an information science,” says Dr. Yang Huanming, cofounder and president of BGI. “If we accept that [genomics] builds on the digitalization of life, then all kinds of genetic information potentially holds value.”

BGI didn’t always seem destined for success—or even survival. “The crazy guys” was how Chinese colleagues initially referred to the two founders, Huanming and director Wang Jian. Refused government support, they muscled their way into the international Human Genome Project, mapping out 1 percent of that celebrated first full sequence before tackling the rice-plant genome on their own, beating a well-funded international consortium, and suddenly finding political leverage. Yang and Wang used it to set up the research center, which is nominally nonprofit but carries out commercial activities in support of the research. With an annual grant of $3 million from the local government in exchange for moving to the shoe factory in 2007, BGI first grew modestly, generating income from fee-for-service sequencing and conducting molecular diagnostic tests for hospitals. A $1.5 billion loan from the Chinese Development Bank in 2009 allowed the company to catapult into a different league, and its combination of sequencing power and advanced DNA data-management solutions for the pharma industry are now drawing international attention. Last year, pharmaceutical giant Merck announced plans for a research collaboration with BGI, as the Chinese company’s revenue hit $150 million—revenue projected to triple this year. “I admire their passion and the willingness to take risks,” says Steven Hsu, a physicist at the University of Oregon, adding that “it permeates the organization.”

... Li Yingrui, 24, directs the bioinformatics department and its 1,500 computer scientists. Having dropped out of college because it didn’t present enough of an intellectual challenge, he firmly believes in motivating young employees with wide-ranging freedom and responsibility. “They grow with the task and develop faster,” he says. One of his researchers is 18-year-old Zhao Bowen. While still in high school, Zhao joined the bioinformatics team for a summer project and blew everyone away with his problem-solving skills. After consulting with his parents, he took a full-time job as a researcher and finished school during his downtime. Fittingly, he now manages a project on the genetic basis of high IQ. His team is sampling 1,000 Chinese adults with an IQ higher than 145, comparing their genomes with those of an equal number of randomly picked control subjects. Zhao acknowledges that such projects linking intelligence with genes may be controversial but “more so elsewhere than in China,” he says, adding that several U.S. research groups have contacted him for collaboration. “Everybody is interested in intelligence,” he says.

A shoe factory becoming a genomics center, scientists replacing blue-collar workers—the Shenzhen research facility embodies the country’s economic and social ambitions. According to a 2010 report from Monitor Group, a management consulting firm based in Boston, China is “poised to become the global leader in life-science discovery and innovation within the next decade.”

... Yang, for his part, puts it simply: “Genomics is international,” he says. “We must collaborate to survive and develop.” Certainly, the scientists at his Shenzhen headquarters have their view on the world. The latest shipment of high-tech toys sits, still unpacked, on the floor; the stamp on the sides of the crates proclaiming: Made in the USA.

15 comments:

botti
said...

Cool, I was just about to mention Razib had also mentioned you and this article on his site. Also, you'd think people would clarify whether someone is Steven or Stephen? I see Steven Pinker often referred to as Stephen.

***Zhao acknowledges that such projects linking intelligence with genes may be controversial but “more so elsewhere than in China,” he says, adding that several U.S. research groups have contacted him for collaboration. ***

I see that a couple of criminologists have a paper out on genetic variation & school verbal iq results.

"The current study partially addresses this gap in the literature by examining whether average IQ scores across thirty-six schools are associated with differences in the allelic distributions of dopaminergic polymorphisms across schools...

The analysis begins by first estimating the association between each of the dopaminergic polymorphisms and individual-level IQ scores. Table 1 presents the means, standard deviations, sample sizes, and correlations for each of the genotypes. The results indicate that DAT1 and DRD2 maintain statistically significant and negative associations with IQ scores, while the effect of DRD4 on IQ is non-significant. To further explore the association between dopaminergic polymorphisms and IQ, we employed the additive dopamine scale as a predictor of IQ scores. The results of this analysis indicated a statistically significant and negative association between IQ and dopamine scores, where higher scores on the dopamine index correspond to lower IQ scores (r=−.15, pb.05, two-tailed test)."

Steve, what do you make of these findings . I never got the "NE Asians are unconscientious neurotics" vibe....but you seem to dabble in the personality research, so maybe you could offer an interpretation.

Steve, do you know why BGI is going the 1,000 extreme case vs random controls route for studying IQ genes? From what I've read most researchers think that large (100,000s) full sequencing studies are the way to go.

Full sequencing of 100k+ people is expensive and it's not easy to get the phenotype measurement here. If you have a ready supply of extreme cases you can save money on sequencing and on administering IQ tests. You have to do some math to figure out the relative power of the two designs.

It's question of statistical power. He didn't have many outliers. You can get those either by selection or having a huge sample size. In any case, the percentage of variance in genes that are explicitly identified is likely to be small for some time to come. However, by using a different kind of analysis one can estimate total variance accounted for by, e.g., the entire SNP set and that is significant in the case of, e.g., height.

Genetic mapping has advanced with the world’s first anatomically and genomically comprehensive human brain map. Here is an article covering this innovation. http://www.americanbiotechnologist.com/blog/gene-map-human-brain/

Genetic mapping has advanced with the world’s first anatomically and genomically comprehensive human brain map. Here is an article covering this innovation. http://www.americanbiotechnologist.com/blog/gene-map-human-brain/